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Charcot worked and taught at the famous Salpêtrière Hospital for more than thirty years. His reputation as an instructor drew students from all over Europe. In 1882, he established a neurology clinic at Salpêtrière, which was the first of its kind in Europe.

Charcot's primary focus was neurology. He was the first to describe a disorder known as Charcot joint or Charcot arthropathy, a degeneration of joint surfaces resulting in loss of proprioception. He researched the functions of different parts of the brain and the role of arteries in cerebral hemorrhage.

He was also one of the first to describe Charcot-Marie-Tooth disease (CMT). The announcement was made simultaneously with Pierre Marie of France (his resident) and Howard Henry Tooth of England. The disease is also sometimes called peroneal muscular atrophy.

But Charcot's most enduring work is that on hypnosis and hysteria. Charcot believed that hysteria was a neurological disorder caused by hereditary problems in the nervous system. He used hypnosis to induce a state of hysteria in patients and studied the results, and was single-handedly responsible for changing the French medical community's opinion about the validity of hypnosis (it was previously rejected as Mesmerism).